Hi Eddie,
I saw you made an other post (here)[http://www.jrpass.com/nl/forum/topics/general-japan-travel/posts/1st-time-to-tokyo] as well, looking at the similarities I've put the answers together in this topic.
Here's a little oversight of ticket costs if you buy them without the JR-Pass.
Tokyo --> Odawara :¥ 3,640
Odawara --> Takayama ¥ 12,410
Takayama --> Tokyo ¥ 14,300
Tokyo --> Narita ¥ 27,40
For a total of:¥ 33.090. The JR-Pass is ¥ 28300, saving you ¥ 4790 + Local travel you may do in Tokyo.
When you go to Hakone you can use your JR-Pass as far as Odawara, from here I would recommend buying a (Hakone Freepass)[http://www.odakyu.jp/english/freepass/hakone_01.html] for 3 days. It costs 4.400 Yen and will cover all your travel there, plus it gives you many discounts on attractions.
Just a little recommendation:
When you are in Takayama, try some of the Hida beef that is served in the area is many restaurants, it's very good!
Hope this helps!
-Daniel